Zeitschriftenartikel: „Control sequence“

1

Elacqua, Elizabeth, Stephen J. Koehler, and Jinzhen Hu. "Electronically Governed ROMP: Expanding Sequence Control for Donor–Acceptor Conjugated Polymers." Synlett 31, no. 15 (2020): 1435–42. http://dx.doi.org/10.1055/s-0040-1707180.

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Controlling the primary sequence of synthetic polymers remains a grand challenge in chemistry. A variety of methods that exert control over monomer sequence have been realized wherein differential reactivity, pre-organization, and stimuli-response have been key factors in programming sequence. Whereas much has been established in nonconjugated systems, π-extended frameworks remain systems wherein subtle structural changes influence bulk properties. The recent introduction of electronically biased ring-opening metathesis polymerization (ROMP) extends the repertoire of feasible approaches to prescribe donor–acceptor sequences in conjugated polymers, by enabling a system to achieve both low dispersity and controlled polymer sequences. Herein, we discuss recent advances in obtaining well-defined (i.e., low dispersity) polymers featuring donor–acceptor sequence control, and present our design of an electronically ambiguous (4-methoxy-1-(2-ethylhexyloxy) and benzothiadiazole-(donor–acceptor-)based [2.2]paracyclophanediene monomer that undergoes electronically dictated ROMP. The resultant donor–acceptor polymers were well-defined (Đ = 1.2, Mn > 20 k) and exhibited lower energy excitation and emission in comparison to ‘sequence-ill-defined’ polymers. Electronically driven ROMP expands on prior synthetic methods to attain sequence control, while providing a promising platform for further interrogation of polymer sequence and resultant properties.1 Introduction to Sequence Control2 Sequence Control in Polymers3 Multistep-Synthesis-Driven Sequence Control4 Catalyst-Dictated Sequence Control5 Electronically Governed Sequence Control6 Conclusions

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Fatchiyah, Fatchiyah, Rista Nikmatu Rohmah, Lidwina Faraline Tripisila, et al. "Three-dimension Glyceraldehyde-3-Phosphate Dehydrogenase protein structure of substitution and insertion sequences of GAPDH gene of chicken drumstick meat (Gallus gallus)." Berkala Penelitian Hayati 27, no. 2 (2022): 105–9. http://dx.doi.org/10.23869/bphjbr.27.2.20228.

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The study aimed to observed the 3-D structure of GAPDH protein and identify the GAPDH gene sequences mutation of chicken drumstick meat (Gallus gallus). The sample of chicken meat was randomly taken in four districts in Malang city. In this study, the DNA was isolated from drumstick meat chicken samples, amplified using proper primers, and then sequenced using ABI 3730xl DNA Sequencer. The DNA sequences alignments analyzed by BioEdit software and the control sequence of GAPDH gene was obtained from NCBI GenBank (sequence Gene ID: 374193). Then, the amino acid sequence and 3D structure of GAPDH protein were determined based on the change of nucleotide sequences using Swiss model and PyMol software. The nucleotide sequence of a partially GAPDH gene of drumstick meat chicken from districts two is completely different with a 97 percent similarity level, which found twelve nucleotides’ substitutions mutation between nucleotide base number 354 until 777 and three nucleotides inserted between T753 and G754 nucleotide base. These mutations changed the amino acid sequence and 3D structure of GAPDH protein. This result suggests that the differential drumstick chicken meat GAPDH sequences and 3D structure may induce the change of protein-protein interaction and induction.

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3

Buehler, Deborah M., and Allan J. Baker. "Characterization of the red knot (Calidris canutus) mitochondrial control region." Genome 46, no. 4 (2003): 565–72. http://dx.doi.org/10.1139/g03-034.

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We sequenced the complete mitochondrial control regions of 11 red knots (Calidris canutus). The control region is 1168 bp in length and is flanked by tRNA glutamate (glu) and the gene ND6 at its 5' end and tRNA phenylalanine (phe) and the gene 12S on its 3' end. The sequence possesses conserved sequence blocks F, E, D, C, CSB-1, and the bird similarity box (BSB), as expected for a mitochondrial copy. Flanking tRNA regions show correct secondary structure, and a relative rate test indicated no significant difference between substitution rates in the sequence we obtained versus the known mitochondrial sequence of turnstones (Charadriiformes: Scolopacidae). These characteristics indicate that the sequence is mitochondrial in origin. To confirm this, we sequenced the control region of a single individual using both purified mitochondrial DNA and genomic DNA. The sequences were identical using both methods. The sequence and methods presented in this paper may now serve as a reference for future studies using knot and other avian control regions. Furthermore, the discovery of five variable sites in 11 knots towards the 3' end of the control region, and the variability of this region in contrast to the more conserved central domain in the alignment between knots and other Charadriiformes, highlights the importance of this area as a source of variation for future studies in knots and other birds.Key words: D-loop, Calidris canutus, Charadriiformes, Aves, evolution.

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Liu, Huanzhang, Chyng-Shyan Tzeng, and Hui-Yu Teng. "Sequence variations in the mitochondrial DNA control region and their implications for the phylogeny of the Cypriniformes." Canadian Journal of Zoology 80, no. 3 (2002): 569–81. http://dx.doi.org/10.1139/z02-035.

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The mitochondrial DNA control region of six cobitids and two catostomids was sequenced and compared with sequences of other cypriniforms to study their sequence variations. The extended termination associated sequence (ETAS) domain, central domain, and conserved sequence block (CSB) domain were partitioned and the ETAS sequence, CSB-D, CSB-E, ECSB-F, CSB1, CSB2, and CSB3 were identified. It is suggested that the "hairpin" TACAT-ATGTA is the key sequence of ETAS and GACATA is the symbol of CSB1. Phylogenetic analysis based on the CSB domain showed that all cyprinids evolved as one monophyletic group, while the non-cyprinid Cypriniformes could be another monophyly that is in accordance with the hypothesis proposed by Siebert. Further analysis of the phylogeny of the Cobitoidei was also conducted and it is tentatively suggested that their relationships are Catostomidae + (Gyrinocheilidae + (Botiinae + (Homalopteridae + (Cobitinae + Nemacheilinae)))).

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Quevedo, Daniel E., and Vijay Gupta. "Sequence-Based Anytime Control." IEEE Transactions on Automatic Control 58, no. 2 (2013): 377–90. http://dx.doi.org/10.1109/tac.2012.2209977.

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6

Melo, Princess Marie B. "An Enhanced Transmission Control Protocol Initial Sequence Number Steganographic Method." Journal of Advanced Research in Dynamical and Control Systems 12, no. 01-Special Issue (2020): 252–59. http://dx.doi.org/10.5373/jardcs/v12sp1/20201070.

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7

Stromer, Robert, and Harry A. Mackay. "Conditional Stimulus Control of Childrens' Sequence Production." Psychological Reports 70, no. 3 (1992): 903–12. http://dx.doi.org/10.2466/pr0.1992.70.3.903.

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Normally capable children were first taught to touch in sequence each of a set of five physically dissimilar stimuli (Sequence A). Another set of stimuli was then used to train sequence B. Next, direct training established conditional control of the production of the A sequence and its reversal: in the presence of one printed word, touching the stimuli in the order A1→A2→A3→A4→A5 was reinforced; in the presence of another word, touching the stimuli in the order A5→A4→A3→A2→A1 was reinforced. During probe sessions, the printed words also exercised conditional control over production of the B sequence and its reversal for five of six subjects, suggesting the formation of stimulus classes. Four of these five subjects also performed mixed sequences under conditional control of the words (e.g., A1→B2→A3→B4→A5 and its reversal), verifying that the stimuli which occupied the same position in each sequence were members of the same class.

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STEFANNI, S., I. S. CHEN, and P. J. MILLER. "A very compact mt-DNA control region in the widely distributed goby Pomatoschistus minutus (Teleostei: Gobiidae)." Journal of the Marine Biological Association of the United Kingdom 82, no. 6 (2002): 1001–3. http://dx.doi.org/10.1017/s0025315402006525.

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The control region of the mitochondrial genome was amplified and sequenced for six individuals of the gobioid fish Pomatoschistus minutus, from several European localities, and one specimen of the related Deltentosteus quadrimaculatus. The length of this region for the former species was found to be 773 bp, 7·1% shorter than that previously described as the most compact D-loop known among teleosts. Sequences from other fish have been compared and the largest gap falls in the section between the conserved sequence block and the pyrimidine tract. Alignment of P. minutus sequences was done with D. quadrimaculatus, whose control region length was 853 bp, and this gap was found to be of 61 bp. For the P. minutus sample, the intraspecific sequence divergence is 0·07%.

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Choi, Heejin, and Minsoo Hahn. "Sequence-to-Sequence Emotional Voice Conversion With Strength Control." IEEE Access 9 (2021): 42674–87. http://dx.doi.org/10.1109/access.2021.3065460.

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10

Shih, Y. Y., and D. Chao. "Sequence of Control in S3PMR." Computer Journal 53, no. 10 (2009): 1691–703. http://dx.doi.org/10.1093/comjnl/bxp081.

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11

Badi, Nezha, and Jean-François Lutz. "Sequence control in polymer synthesis." Chemical Society Reviews 38, no. 12 (2009): 3383. http://dx.doi.org/10.1039/b806413j.

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12

Ozguner, U. "Three-course control laboratory sequence." IEEE Control Systems Magazine 9, no. 3 (1989): 14–18. http://dx.doi.org/10.1109/37.24806.

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13

Ampini, Dieudonne, and Mabonzo Vital Delmas. "Existence of Optimal Control for a Nonlinear Partial Differential Equation of Hyperbolic Type." European Journal of Pure and Applied Mathematics 12, no. 4 (2019): 1595–601. http://dx.doi.org/10.29020/nybg.ejpam.v12i4.3577.

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In this paper, we prove the existence of an optimal control for a nonlinear hyperbolic problem, examined in [3]. An estimation is used which makes it possible to extract from a minimizable sequence of controls and from the sequence of corresponding solutions weakly convergent sub sequences. To prove the passage to the limit in a true equality for every element of the minimizable sequence, Lebesgue’s theorem on the passage to the limit under the integral sign and the theorem of immersion have been used.

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Dueñas, Juan C. Rondan, Cristina N. Gardenal, Guillermo Albrieu Llinás, and Graciela M. Panzetta-Dutari. "Structural organization of the mitochondrial DNA control region in Aedes aegypti." Genome 49, no. 8 (2006): 931–37. http://dx.doi.org/10.1139/g06-053.

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The complete A+T - rich region of Aedes aegypti mitochondrial DNA has been cloned and sequenced. In Argentinean populations of the species, a polymorphism in the length of the amplified fragment was observed. Nucleotide sequence comparison of the shortest and longest A+T - rich amplified fragments detected revealed the presence of 2 types of tandemly repeated blocks. The size variation observed in natural populations is mainly due to the presence of a variable number of a 181 bp tandem repeat unit, located toward the 12S rRNA gene end. The size of the longest A+T - rich region was of 2070 bp, representing the largest control sequence reported for any mosquito species. Few relevant short blocks of primary-sequence similarity conserved in the control region of mosquitoes and other insects were detected scattered throughout the whole region. Five putative stem-loop secondary structures were found, one of them flanked by conserved sequences described in other insects. Our results suggest that there are no universal models of structure–function relations in the control region of insect mtDNA. In addition, we identified a short A+T - rich variable segment in the Ae. aegyti control region that would be suitable for population genetic studies.Key words: mitochondrial DNA, A+T - rich region, repeated elements, conserved blocks, Aedes aegypti.

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Perkin, Lindsey C., Timothy P. L. Smith, and Brenda Oppert. "Variants in the Mitochondrial Genome Sequence of Rhyzopertha dominica (Fabricius) (Coleoptera: Bostrycidae)." Insects 12, no. 5 (2021): 387. http://dx.doi.org/10.3390/insects12050387.

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The lesser grain borer, Rhyzopertha dominica, is a coleopteran pest of stored grains and is mainly controlled by phosphine fumigation, but the increase in phosphine-resistant populations threatens efficacy. Some phosphine-resistant insects have reduced respiration, and thus studying the mitochondrial genome may provide additional information regarding resistance. Genomic DNA from an inbred laboratory strain of R. dominica was extracted and sequenced with both short (Illumina) and long (Pacific Biosciences) read technologies for whole genome sequence assembly and annotation. Short read sequences were assembled and annotated by open software to identify mitochondrial sequences, and the assembled sequence was manually annotated and verified by long read sequences. The mitochondrial genome sequence for R. dominica had a total length of 15,724 bp and encoded 22 trna genes, 2 rRNA genes, 13 protein coding genes (7 nad subunits, 3 cox, 2 atp, and 1 cytB), flanked by a long control region. We compared our predicted mitochondrial genome to that of another from a R. dominica strain from Jingziguan (China). While there was mostly agreement between the two assemblies, key differences will be further examined to determine if mutations in populations are related to insecticide control pressure, mainly that of phosphine. Differences in sequence data, assembly, and annotation also may result in different genome interpretations.

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Martin, B. K., and J. H. Weis. "Functional identification of transcription control sequences of the mouse Crry gene." Journal of Immunology 151, no. 2 (1993): 857–69. http://dx.doi.org/10.4049/jimmunol.151.2.857.

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Abstract The mouse C receptor-related gene Crry is expressed by a wide variety of cells. Those sequences required for the transcriptional control of this gene were identified by deletion analysis of regions 5' of the initiating ATG. Fusion of Crry promoter sequences to the reporter gene CAT identified a region approximately 1,500 bp upstream of the transcriptional start site that enhanced transcription of this gene construct. Gel shift and methylation interference assays were performed, and a specific protein-DNA complex was identified within this region. These assays defined a 16-bp sequence 1,642 bp 5' of the initiating ATG that bound a protein in nuclear extracts prepared from all murine cell lines and tissues examined. The methylation interference assay indicated that the core region of the DNA sequence recognized by the protein was GGAA, the common core binding site for the ets family of proto-oncogenes. Oligonucleotides prepared from this sequence with the GGAA sequence did inhibit the DNA/protein complex formation, whereas those with a mutant GGAA sites did not. The minimal site identified by methylation interference was able to up-regulate transcription when placed downstream of a heterologous promoter, whereas the same sequence with an altered GGAA site could not. Thus, this site functions as an enhancer.

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Tverdokhlebov, V. A. "Models of Functional Dependencies of Elements in Sequences for Solving Problems of Control and Management." Mekhatronika, Avtomatizatsiya, Upravlenie 20, no. 10 (2019): 579–88. http://dx.doi.org/10.17587/mau.20.579-588.

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In paper developed version of the basic concepts, models and methods for the formulation and solution of problems of control and diagnosing of processes in systems, tasks of constructing models of processes in which the causal relationships of events are transformed into functional dependencies between elements in sequences, problems of formalizing of process control rules, etc. For this extended classical recurrent definition of the sequences, which presents the functional elements depending on the immediately preceding to them m elements to offered Z-recurrent definition, which defines the functional relationship between sets of elements in the sequence. The orders of Z-recurrent forms have the form of a set of numbers and are convenient for accurate and complete characterization of the connections of events in processes. The tasks of control, diagnosing, constructing new models of processes, assessing the complexity of processes and rules for managing processes can be formulated and solved using numerical indicators of Z-recurrent definitions. A classification of Z-recurrent definitions of sequences and a classification of processes are constructed, an algorithm for checking the feasibility of determining a Z-recurrent form for given sequences of form is developed. The Z-recurrent definition of sequence is complemented by the Z-recurrent sequence pattern method, which includes: introducing a linear order on the base set of sequence elements, constructing an image for the sequence in the form of a sequence of executing or non-executing relationships between the elements represented by a linear order, and applying Z-recurrent definitions to the constructed image of the sequence. The problem on which the solution of the considered problems is based is the recognition of two sequences by properties, which are determined by the indicators of Z-recurrent definitions of sequences, which have the form of orders of Z-recurrent forms. Sets of orders in executing or non-executing Z-recurrent forms characterize the sequences and the analyzed sets of sequences, which allows you to set and solve problems related to system management: problems of control and diagnosing of processes in the system, problems of constructing process models, problems of formalizing and complexity estimation of control rules of processes.

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Sanson, Gerdine F. O., and Marcelo R. S. Briones. "Typing of Candida glabrata in Clinical Isolates by Comparative Sequence Analysis of the Cytochrome c Oxidase Subunit 2 Gene Distinguishes Two Clusters of Strains Associated with Geographical Sequence Polymorphisms." Journal of Clinical Microbiology 38, no. 1 (2000): 227–35. http://dx.doi.org/10.1128/jcm.38.1.227-235.2000.

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ABSTRACT We tested whether comparative sequence analysis of the mitochondrion-encoded cytochrome c oxidase subunit 2 gene ( COX2 ) could be used to distinguish intraspecific variants of Candida glabrata . Mitochondrial genes are suitable for investigation of close phylogenetic relationships because they evolve much faster than nuclear genes, which in general exhibit very limited intraspecific variation. For this survey we used 11 clinical isolates of C. glabrata from three different geographical locations in Brazil, 10 isolates from one location in the United States, 1 American Type Culture Collection strain as an internal control, and the published sequence of strain CBS 138. The complete coding region of COX2 was amplified from total cellular DNA, and both strands were sequenced twice for each strain. These sequences were aligned with published sequences from other fungi, and the numbers of substitutions and phylogenetic relationships were determined. Typing of these strains was done by using 17 substitutions, with 8 being nonsynonymous and 9 being synonymous. Also, cDNAs made from purified mitochondrial polyadenylated RNA were sequenced to confirm that our sequences correspond to the expressed copies and not nuclear pseudogenes and that a frameshift mutation exists in the 3′ end of the coding region (position 673) relative to the Saccharomyces cerevisiae sequence and the previously published C. glabrata sequence. We estimated the average evolutionary rate of COX2 to be 11.4% sequence divergence/10 8 years and that phylogenetic relationships of yeasts based on these sequences are consistent with rRNA sequence data. Our analysis of COX2 sequences enables typing of C. glabrata strains based on 13 haplotypes and suggests that positions 51 and 519 indicate a geographical polymorphism that discriminates strains isolated in the United States and strains isolated in Brazil. This provides for the first time a means of typing of Candida strains that cause infections by use of direct sequence comparisons and the associated divergence estimates.

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Bo, J., and R. D. Seidler. "Visuospatial Working Memory Capacity Predicts the Organization of Acquired Explicit Motor Sequences." Journal of Neurophysiology 101, no. 6 (2009): 3116–25. http://dx.doi.org/10.1152/jn.00006.2009.

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Studies have suggested that cognitive processes such as working memory and temporal control contribute to motor sequence learning. These processes engage overlapping brain regions with sequence learning, but concrete evidence has been lacking. In this study, we determined whether limits in visuospatial working memory capacity and temporal control abilities affect the temporal organization of explicitly acquired motor sequences. Participants performed an explicit sequence learning task, a visuospatial working memory task, and a continuous tapping timing task. We found that visuospatial working memory capacity, but not the CV from the timing task, correlated with the rate of motor sequence learning and the chunking pattern observed in the learned sequence. These results show that individual differences in short-term visuospatial working memory capacity, but not temporal control, predict the temporal structure of explicitly acquired motor sequences.

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Shon, Sudeok, Alan S. Kwan, and Seungjae Lee. "Shape control of cable structures considering concurrent/sequence control." Structural Engineering and Mechanics 52, no. 5 (2014): 919–35. http://dx.doi.org/10.12989/sem.2014.52.5.919.

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EGNER, T. "Congruency sequence effects and cognitive control." Cognitive, Affective, & Behavioral Neuroscience 7, no. 4 (2007): 380–90. http://dx.doi.org/10.3758/cabn.7.4.380.

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22

Chambers, W. G., and J. Dj Golić. "Fast reconstruction of clock-control sequence." Electronics Letters 38, no. 20 (2002): 1174. http://dx.doi.org/10.1049/el:20020799.

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23

Wilkinson, Leonora, and David R. Shanks. "Intentional Control and Implicit Sequence Learning." Journal of Experimental Psychology: Learning, Memory, and Cognition 30, no. 2 (2004): 354–69. http://dx.doi.org/10.1037/0278-7393.30.2.354.

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Chen, Kanglin, and Dirk A. Lorenz. "Image Sequence Interpolation Using Optimal Control." Journal of Mathematical Imaging and Vision 41, no. 3 (2011): 222–38. http://dx.doi.org/10.1007/s10851-011-0274-2.

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von Brasch, Thomas, Johan Byström, and Lars Petter Lystad. "Optimal Control and the Fibonacci Sequence." Journal of Optimization Theory and Applications 154, no. 3 (2012): 857–78. http://dx.doi.org/10.1007/s10957-012-0061-2.

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Mellmann, Alexander, Paal Skytt Andersen, Stefan Bletz, et al. "High Interlaboratory Reproducibility and Accuracy of Next-Generation-Sequencing-Based Bacterial Genotyping in a Ring Trial." Journal of Clinical Microbiology 55, no. 3 (2017): 908–13. http://dx.doi.org/10.1128/jcm.02242-16.

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ABSTRACTToday, next-generation whole-genome sequencing (WGS) is increasingly used to determine the genetic relationships of bacteria on a nearly whole-genome level for infection control purposes and molecular surveillance. Here, we conducted a multicenter ring trial comprising five laboratories to determine the reproducibility and accuracy of WGS-based typing. The participating laboratories sequenced 20 blind-codedStaphylococcus aureusDNA samples using 250-bp paired-end chemistry for library preparation in a single sequencing run on an Illumina MiSeq sequencer. The run acceptance criteria were sequencing outputs >5.6 Gb and Q30 read quality scores of >75%. Subsequently, spa typing, multilocus sequence typing (MLST), ribosomal MLST, and core genome MLST (cgMLST) were performed by the participants. Moreover, discrepancies in cgMLST target sequences in comparisons with the included and also published sequence of the quality control strain ATCC 25923 were resolved using Sanger sequencing. All five laboratories fulfilled the run acceptance criteria in a single sequencing run without any repetition. Of the 400 total possible typing results, 394 of the reported spa types, sequence types (STs), ribosomal STs (rSTs), and cgMLST cluster types were correct and identical among all laboratories; only six typing results were missing. An analysis of cgMLST allelic profiles corroborated this high reproducibility; only 3 of 183,927 (0.0016%) cgMLST allele calls were wrong. Sanger sequencing confirmed all 12 discrepancies of the ring trial results in comparison with the published sequence of ATCC 25923. In summary, this ring trial demonstrated the high reproducibility and accuracy of current next-generation sequencing-based bacterial typing for molecular surveillance when done with nearly completely locked-down methods.

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Chen, H., R. Vinnakota, and S. J. Flint. "Intragenic activating and repressing elements control transcription from the adenovirus IVa2 initiator." Molecular and Cellular Biology 14, no. 1 (1994): 676–85. http://dx.doi.org/10.1128/mcb.14.1.676-685.1994.

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The downstream stimulatory segment of the adenovirus type 2 IVa promoter includes a TA-rich sequence that binds recombinant TATA-binding proteins (TBP) in vitro. We now demonstrate that when placed upstream of the IVa2, initiator, this TA-rich sequence operated as a TATA element but exhibited significantly lower transcriptional and TBP-binding activities than did the TATA box of the adenovirus major late (ML) promoter. In sharp contrast, changing the IVa2 TA-rich sequence in its natural, intragenic context to the ML TATA sequence increased the activity of the IVa2 promoter only slightly. In view of this discrepancy, we examined the effects of single, double, and clustered point mutations in the downstream sequence on the activity of a minimal IVa2 promoter. Mutations between positions +21 and +29 inhibited IVa2 transcription, in some cases to the very low level directed by the IVa2 initiator alone. By contrast, substitutions within the TA-rich sequence increased the efficiency of IVa2 transcription. These results indicated that the downstream, TA-rich sequence does not function as an intragenic TFIID-binding site but rather is included within a negative regulatory element. Electrophoretic mobility shift and methylation interference assays using wild-type and mutated, intragenic promoter sequences identified a HeLa cell component whose binding to the sequence +11 to +27 correlated with repression of IVa2 transcription, suggesting that a negative regulatory element is superimposed upon the intragenic sequence required for efficient transcription from the IVa2 initiator.

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Chen, H., R. Vinnakota, and S. J. Flint. "Intragenic activating and repressing elements control transcription from the adenovirus IVa2 initiator." Molecular and Cellular Biology 14, no. 1 (1994): 676–85. http://dx.doi.org/10.1128/mcb.14.1.676.

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The downstream stimulatory segment of the adenovirus type 2 IVa promoter includes a TA-rich sequence that binds recombinant TATA-binding proteins (TBP) in vitro. We now demonstrate that when placed upstream of the IVa2, initiator, this TA-rich sequence operated as a TATA element but exhibited significantly lower transcriptional and TBP-binding activities than did the TATA box of the adenovirus major late (ML) promoter. In sharp contrast, changing the IVa2 TA-rich sequence in its natural, intragenic context to the ML TATA sequence increased the activity of the IVa2 promoter only slightly. In view of this discrepancy, we examined the effects of single, double, and clustered point mutations in the downstream sequence on the activity of a minimal IVa2 promoter. Mutations between positions +21 and +29 inhibited IVa2 transcription, in some cases to the very low level directed by the IVa2 initiator alone. By contrast, substitutions within the TA-rich sequence increased the efficiency of IVa2 transcription. These results indicated that the downstream, TA-rich sequence does not function as an intragenic TFIID-binding site but rather is included within a negative regulatory element. Electrophoretic mobility shift and methylation interference assays using wild-type and mutated, intragenic promoter sequences identified a HeLa cell component whose binding to the sequence +11 to +27 correlated with repression of IVa2 transcription, suggesting that a negative regulatory element is superimposed upon the intragenic sequence required for efficient transcription from the IVa2 initiator.

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Farinha, Mark A., and Andrew M. Kropinski. "Overexpression, purification, and analysis of the c1 repressor protein of Pseudomonas aeruginosa bacteriophage D3." Canadian Journal of Microbiology 43, no. 3 (1997): 220–26. http://dx.doi.org/10.1139/m97-030.

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A 3.1-kb region of the bacteriophage D3 genome which contains the immunity functions has recently been sequenced (GenBank accession No. L22692). Sequence analysis indicated the presence of a putative repressor gene (c1) whose protein product functions to maintain the bacteriophage genome as a stably integrated prophage in the chromosome of Pseudomonas aeruginosa. A plasmid was constructed that overexpresses repressor C1 protein under control of Ptac in Escherichia coli. C1 protein was subsequently purified and characterized as a 223 amino acid protein with specific binding affinity for 14-base imperfect palindromic operator sequences located on the genome of bacteriophage D3. N-terminal protein sequence data obtained from automated Edman degradation (16 cycles) of purified repressor protein were identical to the predicted sequence based on DNA sequence analysis of the c1 open reading frame.Key words: promoter, repressor, operator, lambdoid phage, Pseudomonas aeruginosa.

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Cordsmeier, Arne, Christopher Bednar, Sabrina Kübel, Larissa Bauer, and Armin Ensser. "Re-Analysis of the Widely Used Recombinant Murine Cytomegalovirus MCMV-m157luc Derived from the Bacmid pSM3fr Confirms Its Hybrid Nature." International Journal of Molecular Sciences 24, no. 18 (2023): 14102. http://dx.doi.org/10.3390/ijms241814102.

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Murine cytomegalovirus (MCMV), and, in particular, recombinant virus derived from MCMV-bacmid pSM3fr, is widely used as the small animal infection model for human cytomegalovirus (HCMV). We sequenced the complete genomes of MCMV strains and recombinants for quality control. However, we noticed deviances from the deposited reference sequences of MCMV-bacmid pSM3fr. This prompted us to re-analyze pSM3fr and reannotate the reference sequence, as well as that for the commonly used MCMV-m157luc reporter virus. A correct reference sequence for this frequently used pSM3fr, containing a repaired version of m129 (MCK-2) and the luciferase gene instead of ORF m157, was constructed. The new reference also contains the original bacmid sequence, and it has a hybrid origin from MCMV strains Smith and K181.

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Yin, Weiyi, Juan Song, Xiangyu Ren, Qian Yao, Xian Lin, and Ye Dai. "Nonlinear ionization control by temporally shaped fs+ps double-pulse sequence on ZnO." Chinese Optics Letters 21, no. 2 (2023): 021602. http://dx.doi.org/10.3788/col202321.021602.

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32

Imashimizu, Masahiko, Yuji Tokunaga, Ariel Afek, Hiroki Takahashi, Nobuo Shimamoto, and David B. Lukatsky. "Control of Transcription Initiation by Biased Thermal Fluctuations on Repetitive Genomic Sequences." Biomolecules 10, no. 9 (2020): 1299. http://dx.doi.org/10.3390/biom10091299.

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In the process of transcription initiation by RNA polymerase, promoter DNA sequences affect multiple reaction pathways determining the productivity of transcription. However, the question of how the molecular mechanism of transcription initiation depends on the sequence properties of promoter DNA remains poorly understood. Here, combining the statistical mechanical approach with high-throughput sequencing results, we characterize abortive transcription and pausing during transcription initiation by Escherichia coli RNA polymerase at a genome-wide level. Our results suggest that initially transcribed sequences, when enriched with thymine bases, contain the signal for inducing abortive transcription, whereas certain repetitive sequence elements embedded in promoter regions constitute the signal for inducing pausing. Both signals decrease the productivity of transcription initiation. Based on solution NMR and in vitro transcription measurements, we suggest that repetitive sequence elements within the promoter DNA modulate the nonlocal base pair stability of its double-stranded form. This stability profoundly influences the reaction coordinates of the productive initiation via pausing.

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Ritchie, Peter A., and David M. Lambert. "A repeat complex in the mitochondrial control region of Adélie penguins from Antarctica." Genome 43, no. 4 (2000): 613–18. http://dx.doi.org/10.1139/g00-018.

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We have determined the nucleotide sequence of the entire mitochondrial control region (CR) of the Adélie penguin (Pygoscelis adeliae) from Antarctica. Like in most other birds, this CR region is flanked by the gene nad6 and transfer (t)RNA trnE(uuc) at the 5' end and the gene rns and trnF(gaa) at the 3' end. Sequence analysis shows that the Adélie penguin CR contains many elements in common with other CRs including the termination associated sequences (TAS), conserved F, E, D, and C boxes, the conserved sequence block (CSB)-1, as well as the putative light and heavy strand promoters sites (LSP-HSP). We report an extraordinarily long avian control region (1758 bp) which can be attributed to the presence, at the 3' peripheral domain, of five 81-bp repeat sequences, each containing a putative LSP-HSP, followed by 30 tetranucleotide microsatellite repeat sequences consisting of (dC-dA-dA-dA)30. The microsatellite and the 81-bp repeat reside in an area known to be transcribed in other species.Key words: Aves, microsatellite, evolution, D-loop, TAS, WANCY.

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WalkerPeach, Cindy R., Matthew Winkler, Dwight B. DuBois, and Brittan L. Pasloske. "Ribonuclease-resistant RNA Controls (Armored RNA) for Reverse Transcription-PCR, Branched DNA, and Genotyping Assays for Hepatitis C Virus." Clinical Chemistry 45, no. 12 (1999): 2079–85. http://dx.doi.org/10.1093/clinchem/45.12.2079.

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Abstract Background: Comparison and evaluation of molecular diagnostic assays for the detection and quantification of hepatitis C virus (HCV) RNA have been limited by the lack of RNA controls and calibrators. Armored RNA® technology is a means for producing RNA that is completely protected from plasma ribonucleases. This method produces recombinant pseudoviral particles that are noninfectious and contain predefined RNA sequences. Methods: A consensus 412-base sequence from the 5′NCR/Core region of HCV subtype 2b was derived from 34 individually sequenced HCV genotype 2b variants. A DNA fragment encoding the consensus HCV-2b sequence was synthesized de novo, cloned, and expressed as an Armored RNA control. The resulting HCV-2b Armored RNA (AR-HCV-2b) contained the complete HCV-2b consensus RNA sequence encapsidated within a protective protein coat. Results: AR-HCV-2b was fully recoverable from human plasma incubated at 4 °C for &gt;300 days. The particles were tested in three clinical assay formats: AmplicorTM HCV Monitor 1.0, QuantiplexTM HCV RNA 2.0, and INNO-LiPATM HCV II. When added into seronegative, nonviremic plasma, AR-HCV-2b showed reproducible signals and linear dilutions in both the Amplicor and Quantiplex assays. AR-HCV-2b was correctly identified as subtype 2b in the INNO-LiPA line probe assay. Conclusion: The HCV-2b Armored RNA control is a versatile, durable, ribonuclease-resistant viral RNA control that is compatible in three different clinical assay formats.

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He, Xuejun, Feng Lin, Wenkang Huang, Chenxia Li, and Xufeng Jing. "Far-field scattering control of wave based on all-dielectric blazed encoding metagrating." Laser Physics 32, no. 11 (2022): 116204. http://dx.doi.org/10.1088/1555-6611/ac9680.

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Abstract Coding metagrating metasurfaces can realize flexible and effective control of polarization, amplitude, and phase of electromagnetic waves. The coded metagrating builds a bridge between the physical unit structure and the digital coding, and can realize the digital coding calculation processing of the physical device. We propose several all dielectric encoded metagrating sequences, and the detailed analysis of their far-field scattering properties is given. Based on the principle of digital coding addition, we add two coding metagrating sequences to obtain a new coding sequence. This new coding sequence results in an additive integration of the functions of the original two coding sequences. This method provides an idea for the realization of multifunctional devices.

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Kobayashi, Donald Y., Ralph M. Reedy, JulieAnn Bick, and Peter V. Oudemans. "Characterization of a Chitinase Gene from Stenotrophomonas maltophilia Strain 34S1 and Its Involvement in Biological Control." Applied and Environmental Microbiology 68, no. 3 (2002): 1047–54. http://dx.doi.org/10.1128/aem.68.3.1047-1054.2002.

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ABSTRACT A chitinase gene was cloned on a 2.8-kb DNA fragment from Stenotrophomonas maltophilia strain 34S1 by heterologous expression in Burkholderia cepacia. Sequence analysis of this fragment identified an open reading frame encoding a deduced protein of 700 amino acids. Removal of the signal peptide sequence resulted in a predicted protein that was 68 kDa in size. Analysis of the sequence indicated that the chitinase contained a catalytic domain belonging to family 18 of glycosyl hydrolases. Three putative binding domains, a chitin binding domain, a novel polycystic kidney disease (PKD) domain, and a fibronectin type III domain, were also identified within the sequence. Pairwise comparisons of each domain to the most closely related sequences found in database searches clearly demonstrated variation in gene sources and the species from which related sequences originated. A 51-kDa protein with chitinolytic activity was purified from culture filtrates of S. maltophilia strain 34S1 by hydrophobic interaction chromatography. Although the protein was significantly smaller than the size predicted from the sequence, the N-terminal sequence verified that the first 15 amino acids were identical to the deduced sequence of the mature protein encoded by chiA. Marker exchange mutagenesis of chiA resulted in mutant strain C5, which was devoid of chitinolytic activity and lacked the 51-kDa protein in culture filtrates. Strain C5 was also reduced in the ability to suppress summer patch disease on Kentucky bluegrass, supporting a role for the enzyme in the biocontrol activity of S. maltophilia.

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Ananjev, A. V., V. I. Lyutin, and E. V. Lyutina. "Synchronization system of radio pulse sequence during control of object movement." Telecommunications 2023, no. 12 (2023): 18–27. http://dx.doi.org/10.31044/1684-2588-2023-0-12-18-27.

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Based on recurrent algorithms for filtration of Markov sequences, an algorithm for the operation of a synchronization system of a sequence of quasi-periodic radio pulses that occurs in the receiver of an infrared coordinator of an object guidance’s command system with modulated tracer radiation has been synthesized. The analysis of the synthesized algorithms was carried out, during which the quality influence of synchronization by a sequence of pulses on the accuracy of object guidance into a given region of space was determined.

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Dey, Debadeepta, Tian Liu, Boris Sofman, and James Bagnell. "Efficient Optimization of Control Libraries." Proceedings of the AAAI Conference on Artificial Intelligence 26, no. 1 (2021): 1983–89. http://dx.doi.org/10.1609/aaai.v26i1.8383.

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A popular approach to high dimensional control problems in robotics uses a library of candidate “maneuvers” or “trajectories”. The library is either evaluated on a fixed number of candidate choices at runtime (e.g. path set selection for planning) or by iterating through a sequence of feasible choices until success is achieved (e.g. grasp selection). The performance of the library relies heavily on the content and order of the sequence of candidates. We propose a provably efficient method to optimize such libraries, leveraging recent advances in optimizing submodular functions of sequences. This approach is demonstrated on two important problems: mobile robot navigation and manipulator grasp set selection. In the first case, performance can be improved by choosing a subset of candidates which optimizes the metric under consideration (cost of traversal). In the second case, performance can be optimized by minimizing the depth in the list that is searched before a successful candidate is found. Our method can be used in both on-line and batch settings with provable performance guarantees, and can be run in an anytime manner to handle real-time constraints.

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Duharcourt, Sandra, Anne-Marie Keller, and Eric Meyer. "Homology-Dependent Maternal Inhibition of Developmental Excision of Internal Eliminated Sequences inParamecium tetraurelia." Molecular and Cellular Biology 18, no. 12 (1998): 7075–85. http://dx.doi.org/10.1128/mcb.18.12.7075.

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ABSTRACT Thousands of single-copy internal eliminated sequences (IESs) are excised from the germ line genome of ciliates during development of the polygenomic somatic macronucleus, following sexual events.Paramecium IESs are short, noncoding elements that frequently interrupt coding sequences. No absolutely conserved sequence element, other than flanking 5′-TA-3′ direct repeats, has been identified among sequenced IESs; the mechanisms of their specific recognition and precise elimination are unknown. Previous work has revealed the existence of an epigenetic control of excision. It was shown that the presence of one IES in the vegetative macronucleus results in a specific inhibition of the excision of the same element during the development of a new macronucleus, in the following sexual generation. We have assessed the generality and sequence specificity of this transnuclear maternal control by studying the effects of macronuclear transformation with 13 different IESs. We show that at least five of them can be maintained in the new macronuclear genome; sequence specificity is complete both between genes and between different IESs in the same gene. In all cases, the degree of excision inhibition correlates with the copy number of the maternal IES, but each IES shows a characteristic inhibition efficiency. Short internal IES-like segments were found to be excised from two of the IESs when excision between normal boundaries was inhibited. Available data suggest that the sequence specificity of these maternal effects is mediated by pairing interactions between homologous nucleic acids.

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Chen, Wei. "Improved Distributed Model Predictive Control with Control Planning Set." Journal of Control Science and Engineering 2016 (2016): 1–14. http://dx.doi.org/10.1155/2016/8167931.

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We focus on distributed model predictive control algorithm. Each distributed model predictive controller communicates with the others in order to compute the control sequence. But there are not enough communication resources to exchange information between the subsystems because of the limited communication network. This paper presents an improved distributed model predictive control scheme with control planning set. Control planning set algorithm approximates the future control sequences by designed planning set, which can reduce the exchange information among the controllers and can also decrease the distributed MPC controller calculation demand without degrading the whole system performance much. The stability and system performance analysis for distributed model predictive control are given. Simulations of the four-tank control problem and multirobot multitarget tracking problem are illustrated to verify the effectiveness of the proposed control algorithm.

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Zhu, Yinuo, and Youhua Tao. "Sequence-controlled and sequence-defined polypeptoids via the Ugi reaction: synthesis and sequence-driven properties." Polymer Chemistry 12, no. 34 (2021): 4895–902. http://dx.doi.org/10.1039/d1py00658d.

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42

R Nash, Allan, Wendy K Glenn, Stephen S Moore, Judith Kerr, Adrienne R Thompson, and EOP Thompson. "Oestrogen Sulfotransferase: Molecular Cloning and Sequencing of cDNA for the Bovine Placental Enzyme." Australian Journal of Biological Sciences 41, no. 4 (1988): 507. http://dx.doi.org/10.1071/bi9880507.

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The female sex hormone, oestrogen, plays a central role in breast cell proliferation in both the normal and malignant state. It controls transcription from several genes, including that for the progesterone receptor, and in endometrial tissue, via this receptor, it controls the gene for the enzyme oestrogen sulfotransferase. This enzyme may control the level of the oestrogen receptor by sulfurylating free oestradiol. To study the mode of transcriptional control exercised by oestrogen, bovine oestrogen sulfotransferase cDNA has been cloned and the nucleotide sequence determined. The message, of which 1812 bases have been sequenced, contains an open reading frame of 885 bases which encode a protein of 295 amino acids and a maximum apparent molecular weight of 34 600. The deduced protein sequence is supported by existing peptide sequence data and appears to contain a steroid-binding region. Some physico-chemical characteristics of the enzyme appear to differ markedly from those previously reported.

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Cho, Soobum, and Sang Kyu Park. "Optimized Scheduling Technique of Null Subcarriers for Peak Power Control in 3GPP LTE Downlink." Scientific World Journal 2014 (2014): 1–8. http://dx.doi.org/10.1155/2014/279217.

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Orthogonal frequency division multiple access (OFDMA) is a key multiple access technique for the long term evolution (LTE) downlink. However, high peak-to-average power ratio (PAPR) can cause the degradation of power efficiency. The well-known PAPR reduction technique, dummy sequence insertion (DSI), can be a realistic solution because of its structural simplicity. However, the large usage of subcarriers for the dummy sequences may decrease the transmitted data rate in the DSI scheme. In this paper, a novel DSI scheme is applied to the LTE system. Firstly, we obtain the null subcarriers in single-input single-output (SISO) and multiple-input multiple-output (MIMO) systems, respectively; then, optimized dummy sequences are inserted into the obtained null subcarrier. Simulation results show that Walsh-Hadamard transform (WHT) sequence is the best for the dummy sequence and the ratio of 16 to 20 for the WHT and randomly generated sequences has the maximum PAPR reduction performance. The number of near optimal iteration is derived to prevent exhausted iterations. It is also shown that there is no bit error rate (BER) degradation with the proposed technique in LTE downlink system.

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Yu, Shu Chun, Xiao Yang Yu, Jian Ying Fan, and Hai Bin Wu. "Aligning Genomic Sequence Applied in Stereo Matching." Applied Mechanics and Materials 121-126 (October 2011): 4357–61. http://dx.doi.org/10.4028/www.scientific.net/amm.121-126.4357.

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The stereo matching algorithm based on aligning genomic sequence is proposed in the paper. This method is divided in three steps: do genomic sequence on the same name epipolar of stereo matching, get branch matrix by establishing genomic sequences using the same name epipolar after being genomic sequences, control points technology and dynamic backdate method to get disparity. The experimental results show that stereo matching method based on genomic sequences has fast speed and good matching quality.

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Petrella, A., I. Doti, V. Agosti, et al. "A 5′ Regulatory Sequence Containing Two Ets Motifs Controls the Expression of the Wiskott-Aldrich Syndrome Protein (WASP) Gene in Human Hematopoietic Cells." Blood 91, no. 12 (1998): 4554–60. http://dx.doi.org/10.1182/blood.v91.12.4554.

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Abstract The recently-identified Wiskott-Aldrich syndrome protein gene (WASP) is responsible for the Wiskott-Aldrich X-linked immunodeficiency as well as for isolated X-linked thrombocytopenia (XLT). To characterize the regulatory sequences of the WASP gene, we have isolated, sequenced and functionally analyzed a 1.6-Kb DNA fragment upstream of the WASP coding sequence. Transfection experiments showed that this fragment is capable of directing efficient expression of the reporter chloramphenicol acetyltransferase (CAT) gene in all human hematopoietic cell lines tested. Progressive 5′ deletions showed that the minimal sequence required for hematopoietic-specific expression consists of 137 bp upstream of the transcription start site. This contains potential binding sites for several hematopoietic transcription factors and, in particular, two Ets-1 consensus that proved able to specifically bind to proteins present in nuclear extracts of Jurkat cells. Overexpression of Ets-1 in HeLa resulted in transactivation of the CAT reporter gene under the control of WASP regulatory sequences. Disruption of the Ets-binding sequences by side-directed mutagenesis abolished CAT expression in Jurkat cells, indicating that transcription factors of the Ets family play a key role in the control of WASP transcription.

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Petrella, A., I. Doti, V. Agosti, et al. "A 5′ Regulatory Sequence Containing Two Ets Motifs Controls the Expression of the Wiskott-Aldrich Syndrome Protein (WASP) Gene in Human Hematopoietic Cells." Blood 91, no. 12 (1998): 4554–60. http://dx.doi.org/10.1182/blood.v91.12.4554.412k26_4554_4560.

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The recently-identified Wiskott-Aldrich syndrome protein gene (WASP) is responsible for the Wiskott-Aldrich X-linked immunodeficiency as well as for isolated X-linked thrombocytopenia (XLT). To characterize the regulatory sequences of the WASP gene, we have isolated, sequenced and functionally analyzed a 1.6-Kb DNA fragment upstream of the WASP coding sequence. Transfection experiments showed that this fragment is capable of directing efficient expression of the reporter chloramphenicol acetyltransferase (CAT) gene in all human hematopoietic cell lines tested. Progressive 5′ deletions showed that the minimal sequence required for hematopoietic-specific expression consists of 137 bp upstream of the transcription start site. This contains potential binding sites for several hematopoietic transcription factors and, in particular, two Ets-1 consensus that proved able to specifically bind to proteins present in nuclear extracts of Jurkat cells. Overexpression of Ets-1 in HeLa resulted in transactivation of the CAT reporter gene under the control of WASP regulatory sequences. Disruption of the Ets-binding sequences by side-directed mutagenesis abolished CAT expression in Jurkat cells, indicating that transcription factors of the Ets family play a key role in the control of WASP transcription.

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Zhao, G. H., B. Hu, J. K. Song, et al. "Characterization of Oesophagostomum asperum and O. columbianum by internal transcribed spacers of nuclear ribosomal DNA." Journal of Helminthology 88, no. 1 (2012): 74–81. http://dx.doi.org/10.1017/s0022149x12000764.

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AbstractIn the present study, the internal transcribed spacers (ITS) of ribosomal DNA (rDNA) of Oesophagostomum asperum and O. columbianum were amplified and sequenced. The ITS-1, 5.8S and ITS-2 rDNA sequences of O. asperum were 374 bp, 153 bp and 259 bp in length, respectively, and the corresponding sequences of O. columbianum were 259, 153 and 218 bp in length, respectively. Sequence differences in the ITS-1 and ITS-2 rDNA between the two Oesophagostomum species were 9.5–10.2% and 12.7–13.9%, respectively. Sequence differences in the ITS-1 and ITS-2 rDNA among members of the genus Oesophagostomum were 2.5–11.6% and 6.8–22.3%, respectively. Based on genetic markers in the ITS rDNA, an effective polymerase chain reaction (PCR) approach was developed to differentiate O. columbianum from O. asperum with a sensitivity of 0.2 ng/μl DNA. Since accurate characterization of parasites at different taxonomic levels is essential for population genetic studies and control of parasitosis, the present findings have important implications for studying epidemiology, taxonomy and population biology, as well as for the control of oesophagostomiasis.

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Flynn, Loren L., Chalermchai Mitrpant, Abbie Adams, et al. "Targeted SMN Exon Skipping: A Useful Control to Assess In Vitro and In Vivo Splice-Switching Studies." Biomedicines 9, no. 5 (2021): 552. http://dx.doi.org/10.3390/biomedicines9050552.

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The literature surrounding the use of antisense oligonucleotides continues to grow, with new disease and mechanistic applications constantly evolving. Furthermore, the discovery and advancement of novel chemistries continues to improve antisense delivery, stability and effectiveness. For each new application, a rational sequence design is recommended for each oligomer, as is chemistry and delivery optimization. To confirm oligomer delivery and antisense activity, a positive control AO sequence with well characterized target-specific effects is recommended. Here, we describe splice-switching antisense oligomer sequences targeting the ubiquitously expressed human and mouse SMN and Smn genes for use as control AOs for this purpose. We report two AO sequences that induce targeted skipping of SMN1/SMN2 exon 7 and two sequences targeting the Smn gene, that induce skipping of exon 5 and exon 7. These antisense sequences proved effective in inducing alternative splicing in both in vitro and in vivo models and are therefore broadly applicable as controls. Not surprisingly, we discovered a number of differences in efficiency of exon removal between the two species, further highlighting the differences in splice regulation between species.

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Shin, Jacqueline C., and Richard B. Ivry. "Spatial and Temporal Sequence Learning in Patients with Parkinson's Disease or Cerebellar Lesions." Journal of Cognitive Neuroscience 15, no. 8 (2003): 1232–43. http://dx.doi.org/10.1162/089892903322598175.

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The functional role of different subcortical areas in sequence learning is not clear. In the current study, Parkinson's patients, patients with cerebellar damage, and age-matched control participants performed a serial reaction time task in which a spatial sequence and a temporal sequence were presented simultaneously. The responses were based on the spatial sequence, and the temporal sequence was incidental to the task. The two sequences were of the same length, and the phase relationship between them was held constant throughout training. Sequence learning was assessed comparing performance when both sequences were present versus when the dimension of interest was randomized. In addition, sequence integration was assessed by introducing phase-shift blocks. A functional dissociation was found between the two patient groups. Whereas the Parkinson's patients learned the spatial and temporal sequences individually, they did not learn the relationship between the two sequences, suggesting the basal ganglia play a functional role in sequence integration. In contrast, the cerebellar patients did not show any evidence of sequence learning at all, suggesting the cerebellum might play a general role in forming sequential associations.

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Ogert, Robert A., and Karen L. Beemon. "Mutational Analysis of the Rous Sarcoma Virus DR Posttranscriptional Control Element." Journal of Virology 72, no. 4 (1998): 3407–11. http://dx.doi.org/10.1128/jvi.72.4.3407-3411.1998.

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ABSTRACT The direct repeat (DR) sequences flanking the src gene in Rous sarcoma virus are essential posttranscriptional control elements; at least one copy of this sequence is necessary for cytoplasmic accumulation of unspliced viral RNA. These sequences promote Rev-independent human immunodeficiency virus type 1 expression, suggesting they act as constitutive transport elements (CTEs). To determine which regions of this sequence are critical for CTE function, mutations in the downstream DR were generated and tested in a viral deletion construct lacking src and the upstream DR. Two single-point mutations and three different clustered mutations caused substantial reductions in reverse transcriptase activity, Gag protein levels, and unspliced viral RNA in the cytoplasm. Three conserved regions of the CTE, including nucleotides 8844 to 8847, 8862 to 8864, and 8868 to 8870, were most sensitive to inactivation by mutagenesis.

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